In Silico Analysis of Protease Inhibitors in Three Solanaceous Crops Identifies Potential Candidates for...

Phytopathogens and plant pests secrete proteases that facilitate virulence and plant-pest interactions through plant cell protein degradation and potentially through modification of extracellular pathogen proteins. In response, plants produce protease inhibitors (PIs) that bind to and neutralize pest and pathogen proteases, thereby contributing to plant resistance. Solanaceous crops such as potato, tomato, and tobacco contain diverse PIs. We analyzed PIs from 23 wild and domesticated varieties of these crops and identified 3,158 PIs, mostly from potato (77%), followed by tomato (15%) and tobacco (8%). Seven PI families were found: cystatins, PTIIPI, PTIPI, KTPI, MCPI, SERPINs, and Kazal-type SPI, with KTPI being the most prevalent PI. Further domain analysis revealed conserved regions and/or reactive center loop motifs in each PI family, with wild species exhibiting greater diversity in bioactive sites of KTPI and PTIPI compared with domesticated species. After screening for signal peptides and comparing with known PIs, we selected 88 PIs for molecular docking with four proteases from key plant pathogens and pests: metallo, aspartic, cysteine, and trypsin proteases from Pectobacterium carotovorum, Fusarium oxysporum, Meloidogyne incognita, and Helicoverpa armigera, respectively. Molecular docking using HADDOCK and AlphaFold3 prioritized 11 PI candidates with potential bioactivity, with six unique to wild species, suggesting potential for plant disease and pest management.